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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2024-08-01, 20:50 -04 based on data in:

        General Statistics

        Showing 282/282 rows and 4/6 columns.
        Sample Name% Dups% GCMedian Read LengthM Seqs
        ERR1755874_1
        74.9%
        50%
        137bp
        2.7M
        ERR1755874_2
        80.7%
        50%
        137bp
        2.7M
        ERR1755875_1
        72.9%
        49%
        132bp
        1.2M
        ERR1755875_2
        75.1%
        49%
        137bp
        1.2M
        ERR1755883_1
        77.9%
        49%
        127bp
        1.1M
        ERR1755883_2
        74.3%
        49%
        132bp
        1.1M
        ERR1755895_1
        70.9%
        49%
        132bp
        0.5M
        ERR1755895_2
        72.0%
        50%
        132bp
        0.5M
        ERR1755908_1
        68.5%
        49%
        132bp
        1.2M
        ERR1755908_2
        70.2%
        49%
        127bp
        1.2M
        ERR1755910_1
        74.8%
        50%
        122bp
        1.1M
        ERR1755910_2
        72.8%
        50%
        127bp
        1.1M
        ERR1755912_1
        71.6%
        50%
        132bp
        1.2M
        ERR1755912_2
        72.7%
        50%
        127bp
        1.2M
        ERR1755913_1
        74.6%
        50%
        132bp
        0.9M
        ERR1755913_2
        76.7%
        50%
        132bp
        0.9M
        ERR1755917_1
        75.5%
        50%
        122bp
        1.3M
        ERR1755917_2
        76.1%
        51%
        132bp
        1.3M
        ERR1755919_1
        94.7%
        50%
        142bp
        2.0M
        ERR1755919_2
        90.8%
        50%
        137bp
        2.0M
        ERR1755921_1
        77.6%
        48%
        132bp
        1.3M
        ERR1755921_2
        81.1%
        48%
        132bp
        1.3M
        ERR1755922_1
        70.5%
        49%
        122bp
        0.6M
        ERR1755922_2
        71.9%
        49%
        127bp
        0.6M
        ERR1755935_1
        75.6%
        50%
        132bp
        0.9M
        ERR1755935_2
        78.1%
        50%
        132bp
        0.9M
        ERR1755937_1
        72.8%
        50%
        122bp
        1.0M
        ERR1755937_2
        73.0%
        51%
        122bp
        1.0M
        ERR1755940_1
        74.3%
        49%
        127bp
        1.0M
        ERR1755940_2
        73.3%
        50%
        132bp
        1.0M
        ERR1755943_1
        77.1%
        49%
        132bp
        1.6M
        ERR1755943_2
        79.3%
        50%
        137bp
        1.6M
        ERR1755944_1
        74.2%
        49%
        137bp
        0.4M
        ERR1755944_2
        73.8%
        50%
        127bp
        0.4M
        ERR1755946_1
        80.9%
        48%
        132bp
        1.2M
        ERR1755946_2
        81.3%
        49%
        127bp
        1.2M
        ERR1755949_1
        73.6%
        50%
        127bp
        0.8M
        ERR1755949_2
        71.3%
        50%
        132bp
        0.8M
        ERR1755954_1
        68.6%
        48%
        132bp
        0.8M
        ERR1755954_2
        66.2%
        49%
        132bp
        0.8M
        ERR1755957_1
        96.1%
        49%
        132bp
        2.3M
        ERR1755957_2
        93.5%
        49%
        122bp
        2.3M
        ERR1755965_1
        76.3%
        49%
        132bp
        1.6M
        ERR1755965_2
        80.6%
        50%
        142bp
        1.6M
        ERR1755971_1
        86.2%
        50%
        137bp
        1.1M
        ERR1755971_2
        85.9%
        50%
        137bp
        1.1M
        ERR1755973_1
        73.5%
        49%
        137bp
        1.4M
        ERR1755973_2
        79.2%
        49%
        137bp
        1.4M
        ERR1755988_1
        73.8%
        49%
        127bp
        0.6M
        ERR1755988_2
        74.2%
        50%
        122bp
        0.6M
        ERR1755991_1
        71.0%
        49%
        127bp
        1.2M
        ERR1755991_2
        72.8%
        49%
        137bp
        1.2M
        ERR1756002_1
        69.9%
        48%
        127bp
        0.7M
        ERR1756002_2
        74.8%
        49%
        137bp
        0.7M
        ERR1756003_1
        95.9%
        50%
        127bp
        2.3M
        ERR1756003_2
        92.8%
        50%
        122bp
        2.3M
        ERR1756006_1
        75.5%
        47%
        132bp
        1.3M
        ERR1756006_2
        81.4%
        47%
        132bp
        1.3M
        ERR1756007_1
        73.6%
        49%
        132bp
        1.0M
        ERR1756007_2
        75.6%
        49%
        137bp
        1.0M
        ERR1756017_1
        75.8%
        49%
        132bp
        1.3M
        ERR1756017_2
        76.9%
        50%
        127bp
        1.3M
        ERR1756023_1
        81.7%
        49%
        117bp
        3.1M
        ERR1756023_2
        80.6%
        50%
        127bp
        3.1M
        ERR1756032_1
        95.2%
        49%
        151bp
        2.0M
        ERR1756032_2
        95.3%
        49%
        151bp
        2.0M
        ERR1756035_1
        73.9%
        49%
        122bp
        0.9M
        ERR1756035_2
        74.9%
        50%
        122bp
        0.9M
        ERR1756044_1
        78.4%
        47%
        132bp
        1.1M
        ERR1756044_2
        74.6%
        47%
        137bp
        1.1M
        ERR1756057_1
        63.9%
        48%
        142bp
        0.2M
        ERR1756057_2
        64.6%
        49%
        142bp
        0.2M
        ERR1756062_1
        66.7%
        49%
        132bp
        0.5M
        ERR1756062_2
        71.1%
        50%
        132bp
        0.5M
        ERR1756071_1
        77.7%
        49%
        132bp
        0.9M
        ERR1756071_2
        80.6%
        50%
        137bp
        0.9M
        ERR1756073_1
        69.2%
        49%
        127bp
        1.1M
        ERR1756073_2
        72.2%
        49%
        132bp
        1.1M
        ERR1756075_1
        70.0%
        49%
        127bp
        1.1M
        ERR1756075_2
        73.6%
        49%
        137bp
        1.1M
        ERR1756080_1
        84.6%
        50%
        132bp
        1.4M
        ERR1756080_2
        84.0%
        50%
        132bp
        1.4M
        ERR1756084_1
        72.5%
        48%
        127bp
        1.3M
        ERR1756084_2
        74.5%
        48%
        137bp
        1.3M
        ERR1756086_1
        75.1%
        49%
        137bp
        1.4M
        ERR1756086_2
        78.8%
        49%
        142bp
        1.4M
        ERR1756092_1
        69.2%
        50%
        132bp
        1.0M
        ERR1756092_2
        71.0%
        50%
        132bp
        1.0M
        ERR1756095_1
        68.4%
        49%
        132bp
        0.9M
        ERR1756095_2
        70.8%
        49%
        137bp
        0.9M
        ERR1756101_1
        69.5%
        49%
        127bp
        0.9M
        ERR1756101_2
        72.6%
        50%
        127bp
        0.9M
        ERR1756105_1
        90.6%
        49%
        147bp
        4.9M
        ERR1756105_2
        93.8%
        49%
        142bp
        4.9M
        ERR1756107_1
        73.1%
        50%
        137bp
        0.5M
        ERR1756107_2
        72.8%
        50%
        127bp
        0.5M
        ERR1756111_1
        72.2%
        49%
        127bp
        0.9M
        ERR1756111_2
        73.1%
        50%
        122bp
        0.9M
        ERR1756115_1
        95.8%
        49%
        137bp
        2.3M
        ERR1756115_2
        94.5%
        49%
        132bp
        2.3M
        ERR1756118_1
        78.8%
        48%
        137bp
        0.8M
        ERR1756118_2
        80.3%
        49%
        132bp
        0.8M
        ERR1756127_1
        67.3%
        49%
        122bp
        0.8M
        ERR1756127_2
        67.8%
        50%
        132bp
        0.8M
        ERR1756130_1
        76.1%
        49%
        127bp
        1.4M
        ERR1756130_2
        78.8%
        50%
        127bp
        1.4M
        ERR1756131_1
        96.8%
        49%
        132bp
        2.7M
        ERR1756131_2
        94.8%
        49%
        127bp
        2.7M
        ERR1756135_1
        70.5%
        49%
        127bp
        0.9M
        ERR1756135_2
        72.7%
        50%
        132bp
        0.9M
        ERR1756136_1
        75.1%
        49%
        122bp
        0.6M
        ERR1756136_2
        75.1%
        50%
        127bp
        0.6M
        ERR1756138_1
        64.0%
        48%
        132bp
        0.5M
        ERR1756138_2
        67.3%
        49%
        132bp
        0.5M
        ERR1756139_1
        74.6%
        50%
        132bp
        2.0M
        ERR1756139_2
        79.8%
        50%
        137bp
        2.0M
        ERR1756149_1
        69.8%
        49%
        122bp
        0.6M
        ERR1756149_2
        72.3%
        49%
        132bp
        0.6M
        ERR1756161_1
        79.1%
        49%
        132bp
        1.5M
        ERR1756161_2
        81.4%
        49%
        137bp
        1.5M
        ERR1756162_1
        69.7%
        49%
        122bp
        0.9M
        ERR1756162_2
        70.8%
        49%
        132bp
        0.9M
        ERR1756165_1
        71.7%
        49%
        132bp
        0.8M
        ERR1756165_2
        75.7%
        50%
        137bp
        0.8M
        ERR1756169_1
        77.3%
        48%
        132bp
        1.9M
        ERR1756169_2
        81.2%
        49%
        137bp
        1.9M
        ERR1756171_1
        71.0%
        49%
        127bp
        1.2M
        ERR1756171_2
        72.1%
        50%
        132bp
        1.2M
        ERR1756182_1
        95.4%
        49%
        127bp
        2.6M
        ERR1756182_2
        90.1%
        49%
        122bp
        2.6M
        ERR1756183_1
        72.6%
        49%
        137bp
        1.6M
        ERR1756183_2
        79.5%
        49%
        137bp
        1.6M
        ERR1756186_1
        77.4%
        50%
        132bp
        1.4M
        ERR1756186_2
        77.9%
        50%
        127bp
        1.4M
        ERR1756192_1
        69.1%
        49%
        132bp
        0.5M
        ERR1756192_2
        71.9%
        50%
        127bp
        0.5M
        ERR1756203_1
        75.8%
        49%
        122bp
        1.1M
        ERR1756203_2
        75.2%
        50%
        122bp
        1.1M
        ERR1756219_1
        71.2%
        49%
        127bp
        1.3M
        ERR1756219_2
        73.5%
        49%
        137bp
        1.3M
        ERR1756220_1
        95.3%
        49%
        127bp
        2.6M
        ERR1756220_2
        90.5%
        49%
        122bp
        2.6M
        ERR1756221_1
        95.8%
        50%
        127bp
        2.5M
        ERR1756221_2
        93.6%
        50%
        122bp
        2.5M
        ERR1756224_1
        73.2%
        49%
        132bp
        0.6M
        ERR1756224_2
        76.6%
        50%
        137bp
        0.6M
        ERR1756228_1
        77.3%
        50%
        127bp
        1.0M
        ERR1756228_2
        78.0%
        50%
        132bp
        1.0M
        ERR1756232_1
        76.7%
        49%
        132bp
        1.1M
        ERR1756232_2
        78.6%
        49%
        137bp
        1.1M
        ERR1756234_1
        93.7%
        50%
        137bp
        3.0M
        ERR1756234_2
        94.7%
        50%
        137bp
        3.0M
        ERR1756237_1
        64.5%
        49%
        132bp
        0.6M
        ERR1756237_2
        65.7%
        50%
        132bp
        0.6M
        ERR1756243_1
        75.5%
        49%
        132bp
        1.1M
        ERR1756243_2
        71.9%
        49%
        137bp
        1.1M
        ERR1756246_1
        78.2%
        49%
        137bp
        3.6M
        ERR1756246_2
        80.6%
        49%
        137bp
        3.6M
        ERR1756249_1
        70.9%
        49%
        127bp
        1.1M
        ERR1756249_2
        73.5%
        49%
        127bp
        1.1M
        ERR1756250_1
        66.2%
        49%
        132bp
        0.6M
        ERR1756250_2
        67.8%
        49%
        132bp
        0.6M
        ERR1756254_1
        71.0%
        49%
        132bp
        0.8M
        ERR1756254_2
        71.2%
        49%
        137bp
        0.8M
        ERR1756258_1
        70.5%
        49%
        132bp
        1.2M
        ERR1756258_2
        74.3%
        50%
        137bp
        1.2M
        ERR1756259_1
        74.4%
        50%
        122bp
        1.1M
        ERR1756259_2
        74.7%
        50%
        122bp
        1.1M
        ERR1756270_1
        83.5%
        49%
        132bp
        1.8M
        ERR1756270_2
        80.8%
        49%
        132bp
        1.8M
        ERR1756280_1
        83.3%
        49%
        132bp
        2.0M
        ERR1756280_2
        82.4%
        49%
        132bp
        2.0M
        ERR1756293_1
        64.6%
        48%
        142bp
        0.2M
        ERR1756293_2
        65.8%
        48%
        142bp
        0.2M
        ERR1756296_1
        73.2%
        49%
        122bp
        0.9M
        ERR1756296_2
        74.2%
        50%
        122bp
        0.9M
        ERR1756297_1
        76.3%
        50%
        127bp
        2.6M
        ERR1756297_2
        80.9%
        50%
        132bp
        2.6M
        ERR1756300_1
        70.3%
        50%
        132bp
        0.5M
        ERR1756300_2
        73.6%
        50%
        132bp
        0.5M
        ERR1756304_1
        93.7%
        50%
        142bp
        2.0M
        ERR1756304_2
        94.4%
        50%
        142bp
        2.0M
        ERR1756317_1
        69.1%
        47%
        132bp
        0.6M
        ERR1756317_2
        68.3%
        48%
        132bp
        0.6M
        ERR1756327_1
        75.8%
        49%
        127bp
        2.2M
        ERR1756327_2
        77.0%
        49%
        132bp
        2.2M
        ERR1756353_1
        74.1%
        49%
        132bp
        1.3M
        ERR1756353_2
        83.3%
        49%
        137bp
        1.3M
        ERR1756365_1
        91.8%
        49%
        142bp
        4.0M
        ERR1756365_2
        94.3%
        49%
        142bp
        4.0M
        ERR1879918_1
        76.7%
        50%
        132bp
        2.3M
        ERR1879918_2
        79.7%
        50%
        137bp
        2.3M
        ERR562364_1
        97.1%
        47%
        151bp
        2.1M
        ERR562364_2
        96.6%
        47%
        151bp
        2.1M
        ERR562378_1
        96.2%
        50%
        151bp
        2.2M
        ERR562378_2
        89.1%
        50%
        151bp
        2.2M
        ERR562385_1
        97.6%
        51%
        151bp
        2.3M
        ERR562385_2
        94.6%
        51%
        151bp
        2.3M
        ERR562386_1
        95.4%
        50%
        151bp
        2.5M
        ERR562386_2
        89.5%
        50%
        151bp
        2.5M
        ERR562391_1
        96.1%
        49%
        151bp
        2.6M
        ERR562391_2
        89.3%
        50%
        151bp
        2.6M
        ERR562413_1
        90.6%
        50%
        151bp
        2.6M
        ERR562413_2
        80.1%
        50%
        151bp
        2.6M
        ERR562431_1
        97.3%
        50%
        151bp
        2.2M
        ERR562431_2
        95.4%
        50%
        151bp
        2.2M
        ERR562434_1
        96.9%
        50%
        151bp
        2.2M
        ERR562434_2
        94.2%
        50%
        151bp
        2.2M
        ERR562441_1
        97.6%
        53%
        151bp
        2.0M
        ERR562441_2
        96.9%
        52%
        151bp
        2.0M
        ERR562451_1
        82.9%
        49%
        132bp
        2.4M
        ERR562451_2
        86.5%
        49%
        137bp
        2.4M
        ERR562452_1
        96.0%
        49%
        151bp
        2.8M
        ERR562452_2
        92.4%
        49%
        151bp
        2.8M
        ERR562457_1
        96.5%
        49%
        151bp
        2.4M
        ERR562457_2
        94.8%
        49%
        151bp
        2.4M
        ERR562470_1
        94.6%
        48%
        151bp
        0.8M
        ERR562470_2
        92.1%
        48%
        151bp
        0.8M
        ERR562471_1
        75.2%
        50%
        127bp
        0.5M
        ERR562471_2
        72.7%
        50%
        137bp
        0.5M
        ERR562498_1
        97.4%
        50%
        151bp
        3.2M
        ERR562498_2
        96.8%
        49%
        151bp
        3.2M
        ERR562500_1
        96.6%
        50%
        151bp
        1.8M
        ERR562500_2
        94.9%
        51%
        151bp
        1.8M
        ERR562516_1
        96.1%
        49%
        151bp
        1.0M
        ERR562516_2
        93.7%
        49%
        151bp
        1.0M
        ERR562517_1
        96.9%
        50%
        151bp
        1.8M
        ERR562517_2
        95.3%
        50%
        151bp
        1.8M
        ERR562530_1
        94.7%
        49%
        151bp
        2.0M
        ERR562530_2
        88.7%
        49%
        151bp
        2.0M
        ERR562532_1
        95.6%
        50%
        151bp
        2.3M
        ERR562532_2
        93.1%
        50%
        151bp
        2.3M
        ERR562542_1
        98.1%
        50%
        151bp
        3.0M
        ERR562542_2
        96.8%
        50%
        151bp
        3.0M
        ERR562549_1
        96.7%
        50%
        151bp
        3.5M
        ERR562549_2
        94.8%
        50%
        151bp
        3.5M
        ERR562551_1
        90.7%
        49%
        151bp
        2.2M
        ERR562551_2
        81.9%
        49%
        151bp
        2.2M
        ERR562561_1
        60.3%
        49%
        132bp
        0.1M
        ERR562561_2
        73.3%
        49%
        137bp
        0.1M
        ERR562566_1
        95.7%
        50%
        151bp
        2.6M
        ERR562566_2
        90.8%
        50%
        151bp
        2.6M
        ERR562585_1
        95.8%
        50%
        151bp
        0.8M
        ERR562585_2
        92.5%
        50%
        151bp
        0.8M
        ERR562588_1
        96.8%
        50%
        151bp
        3.5M
        ERR562588_2
        94.2%
        50%
        151bp
        3.5M
        ERR562590_1
        97.7%
        47%
        151bp
        2.2M
        ERR562590_2
        97.2%
        47%
        151bp
        2.2M
        ERR562602_1
        84.7%
        49%
        151bp
        0.5M
        ERR562602_2
        89.2%
        49%
        147bp
        0.5M
        ERR562611_1
        96.0%
        50%
        151bp
        1.8M
        ERR562611_2
        91.9%
        50%
        151bp
        1.8M
        ERR562614_1
        97.0%
        51%
        151bp
        2.6M
        ERR562614_2
        96.1%
        50%
        151bp
        2.6M
        ERR562616_1
        96.7%
        48%
        151bp
        2.5M
        ERR562616_2
        95.5%
        48%
        151bp
        2.5M
        ERR562619_1
        95.0%
        50%
        151bp
        2.3M
        ERR562619_2
        88.8%
        50%
        151bp
        2.3M
        ERR562638_1
        96.9%
        49%
        151bp
        2.0M
        ERR562638_2
        94.3%
        49%
        151bp
        2.0M
        ERR562643_1
        96.4%
        49%
        151bp
        2.7M
        ERR562643_2
        89.1%
        50%
        151bp
        2.7M
        ERR562646_1
        95.5%
        50%
        151bp
        2.4M
        ERR562646_2
        90.0%
        50%
        151bp
        2.4M
        ERR562647_1
        97.0%
        50%
        151bp
        3.1M
        ERR562647_2
        94.7%
        50%
        151bp
        3.1M
        ERR562657_1
        97.5%
        49%
        151bp
        1.9M
        ERR562657_2
        96.3%
        49%
        151bp
        1.9M
        ERR562659_1
        97.2%
        50%
        151bp
        3.2M
        ERR562659_2
        95.9%
        50%
        151bp
        3.2M
        ERR562664_1
        96.9%
        49%
        151bp
        1.8M
        ERR562664_2
        95.5%
        49%
        151bp
        1.8M
        ERR562665_1
        95.3%
        50%
        151bp
        1.7M
        ERR562665_2
        91.1%
        50%
        151bp
        1.7M
        ERR562667_1
        89.2%
        48%
        151bp
        2.1M
        ERR562667_2
        78.5%
        48%
        151bp
        2.1M
        ERR562670_1
        96.4%
        50%
        151bp
        2.6M
        ERR562670_2
        94.6%
        49%
        151bp
        2.6M
        ERR562700_1
        97.1%
        49%
        151bp
        2.2M
        ERR562700_2
        95.5%
        49%
        151bp
        2.2M
        ERR562702_1
        96.7%
        47%
        151bp
        1.6M
        ERR562702_2
        95.0%
        47%
        151bp
        1.6M

        FastQC

        Version: 0.11.9

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Created with MultiQC

        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Created with MultiQC

        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Created with MultiQC

        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Created with MultiQC

        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Created with MultiQC

        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Created with MultiQC

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Created with MultiQC

        Overrepresented sequences by sample

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as overrepresented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Created with MultiQC

        Top overrepresented sequences

        Top overrepresented sequences across all samples. The table shows 20 most overrepresented sequences across all samples, ranked by the number of samples they occur in.

        Showing 20/20 rows and 3/3 columns.
        Overrepresented sequenceSamplesOccurrences% of all reads
        CCTTCTGCAGGTTCACCTACGGAAACCTTGTTACGACTTCTCCTTCCTCT
        282
        50537820
        11.1275%
        CCTTCCGCAGGTTCACCTACGGAAACCTTGTTACGACTTCTCCTTCCTCT
        282
        23315667
        5.1337%
        CCTTCTGCAGGTTCACCTACGGAAACCTTGTTACGACTTTTACTTCCTCT
        282
        11869507
        2.6134%
        TTGTACACACCGCCCGTCGCTCCTACCGATTGAGTGATCCGGTGAATAAT
        282
        26613983
        5.8599%
        CCTTCTGCAGGTTCACCTACGGAAACCTTGTTACGACTTCACCTTCCTCT
        282
        10445090
        2.2998%
        CCTTCCGCAGGTTCACCTACGGAAACCTTGTTACGACTTTTACTTCCTCT
        281
        5601856
        1.2334%
        CCTTCCGCAGGTTCACCTACGGAAACCTTGTTACGACTTCACCTTCCTCT
        280
        4774006
        1.0511%
        CCTTCTGCAGGTTCACCTACGGCTACCTTGTTACGACTTCACCCCAGTCG
        277
        5243942
        1.1546%
        CCTTCCGCAGGTTCACCTACGGCTACCTTGTTACGACTTCACCCCAGTCG
        272
        2941095
        0.6476%
        CCTTCTGCAGGTTCACCTACGGCTACCTTGTTACGACTTCACCCCAGTCA
        257
        2507299
        0.5521%
        TTGTACACACCGCCCGTCACACCATGGGAGTTGGTTCTACCTTAAGGCAA
        255
        3909977
        0.8609%
        CCTTCTGCAGGTTCACCTACGGTAACCTTGTTACGACTTCACCTTCCTCT
        237
        1784079
        0.3928%
        TTGTACACACCGCCCGTCGCTCCTACCGATTGAATGATCCGGTGAGGCCC
        229
        2339733
        0.5152%
        TTGTACACACCGCCCGTCGCTCCTACCGATTGAGTGATCCGGTGAATACT
        226
        1656977
        0.3648%
        CCTTCTGCAGGTTCACCTACGGAAACCTTGTTACGACTTTTGCTTCCTCT
        224
        1408703
        0.3102%
        CCTTCCGCAGGTTCACCTACGGCTACCTTGTTACGACTTCACCCCAGTCA
        224
        1347590
        0.2967%
        TTGTACACACCGCCCGTCGCTACTACCGATTGAACGTTTTAGTGAGGTCC
        215
        4104836
        0.9038%
        TTGTACACACCGCCCGTCACACCATGGAAGTTGGTTACACCTTAAGGCAA
        215
        1681902
        0.3703%
        TTGTACACACCGCCCGTCGCTCCTACCGATTGGATGATCCGGTGAATAAT
        213
        2452441
        0.5400%
        TTGTACACACCGCCCGTCGCACCTACCGATTGAATGGTCCGGTGAAATCT
        208
        1491675
        0.3284%

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        Created with MultiQC

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

        Created with MultiQC

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        SoftwareVersion
        FastQC0.11.9

        MultiQC v1.23 - Written by Phil Ewels, available on GitHub.

        This report uses Plotly, jQuery, jQuery UI, Bootstrap, FileSaver.js and clipboard.js.